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GeneBe

SCEL

sciellin, the group of LIM domain containing

Basic information

Region (hg38): 13:77535673-77645263

Links

ENSG00000136155NCBI:8796OMIM:604112HGNC:10573Uniprot:O95171AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCEL gene.

  • Inborn genetic diseases (30 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCEL gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
0
missense
29
clinvar
1
clinvar
30
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 29 1 0

Variants in SCEL

This is a list of pathogenic ClinVar variants found in the SCEL region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
13-77555907-C-T Inborn genetic diseases Uncertain significance (Feb 28, 2023)2490814
13-77556608-C-T Inborn genetic diseases Uncertain significance (May 11, 2022)2288839
13-77556623-C-G Inborn genetic diseases Uncertain significance (Jan 25, 2023)2461469
13-77556625-C-T Inborn genetic diseases Uncertain significance (Dec 19, 2022)2336369
13-77556675-G-C Inborn genetic diseases Uncertain significance (Aug 04, 2021)2241416
13-77556703-G-A Inborn genetic diseases Uncertain significance (Mar 21, 2023)2569036
13-77559817-G-A Moyamoya angiopathy Likely pathogenic (-)982220
13-77559836-G-A Inborn genetic diseases Uncertain significance (Dec 05, 2022)2353431
13-77563849-T-A Inborn genetic diseases Uncertain significance (Dec 14, 2021)2266834
13-77563871-C-T Inborn genetic diseases Uncertain significance (May 31, 2023)2509170
13-77569378-G-A Inborn genetic diseases Uncertain significance (Feb 13, 2023)2483104
13-77572141-C-T Inborn genetic diseases Uncertain significance (Dec 19, 2022)2335675
13-77572186-G-A Inborn genetic diseases Uncertain significance (Feb 15, 2023)2471527
13-77572188-C-T Inborn genetic diseases Uncertain significance (Jun 06, 2022)2344329
13-77591448-A-G Inborn genetic diseases Uncertain significance (Aug 17, 2021)2246395
13-77599712-T-C Inborn genetic diseases Uncertain significance (Jul 09, 2021)2231710
13-77602099-C-G Inborn genetic diseases Uncertain significance (Jun 26, 2023)2603821
13-77602667-G-A Inborn genetic diseases Uncertain significance (Jun 02, 2023)2555627
13-77602704-C-T Inborn genetic diseases Uncertain significance (Feb 06, 2023)2462798
13-77603117-G-A Inborn genetic diseases Uncertain significance (Aug 08, 2022)2305912
13-77604379-T-A Inborn genetic diseases Uncertain significance (Apr 07, 2022)2351318
13-77604412-C-T Inborn genetic diseases Uncertain significance (Aug 17, 2021)2347147
13-77610060-G-A Inborn genetic diseases Uncertain significance (Sep 16, 2021)2349086
13-77617619-T-C Inborn genetic diseases Uncertain significance (Jul 27, 2021)2216263
13-77617648-A-C Inborn genetic diseases Uncertain significance (Oct 25, 2022)2318973

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SCELprotein_codingprotein_codingENST00000349847 32109590
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
4.58e-210.12812547512721257480.00109
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.2863323470.9570.00001674592
Missense in Polyphen89100.790.883051434
Synonymous1.46931130.8250.000005701165
Loss of Function1.503849.40.7690.00000234623

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.01060.0106
Ashkenazi Jewish0.0002140.000198
East Asian0.0001950.000163
Finnish0.0004170.000416
European (Non-Finnish)0.0003740.000360
Middle Eastern0.0001950.000163
South Asian0.0009420.000915
Other0.001170.00114

dbNSFP

Source: dbNSFP

Function
FUNCTION: May function in the assembly or regulation of proteins in the cornified envelope. The LIM domain may be involved in homotypic or heterotypic associations and may function to localize sciellin to the cornified envelope.;

Recessive Scores

pRec
0.109

Intolerance Scores

loftool
0.996
rvis_EVS
0.11
rvis_percentile_EVS
62.1

Haploinsufficiency Scores

pHI
0.0815
hipred
N
hipred_score
0.145
ghis
0.515

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.485

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyHighMediumHigh
CancerHighHighHigh

Mouse Genome Informatics

Gene name
Scel
Phenotype
normal phenotype;

Gene ontology

Biological process
epidermis development;response to mechanical stimulus;embryo development ending in birth or egg hatching;keratinocyte differentiation;positive regulation of canonical Wnt signaling pathway
Cellular component
cornified envelope;cytoplasm;perinuclear region of cytoplasm;extracellular exosome
Molecular function
protein binding;metal ion binding